LAMMPS (13 Oct 2016)
# sample LAMMPS input script for viscosity of 2d LJ liquid
# use shearing wall, thermostat via fix langevin

# settings

variable	x equal 20
variable	y equal 20
variable	ylo equal -2.5
variable	yhi equal 23

variable	rho equal 0.6
variable        t equal 1.0
variable	rc equal 2.5

variable	srate equal 2.7

# problem setup

units		lj
dimension	2
atom_style	atomic
neigh_modify	delay 0 every 1

lattice         sq2 ${rho}
lattice         sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region          simbox block 0 $x ${ylo} ${yhi} -0.1 0.1
region          simbox block 0 20 ${ylo} ${yhi} -0.1 0.1
region          simbox block 0 20 -2.5 ${yhi} -0.1 0.1
region          simbox block 0 20 -2.5 23 -0.1 0.1
create_box      3 simbox
Created orthogonal box = (0 -4.56435 -0.182574) to (36.5148 41.9921 0.182574)
  1 by 1 by 1 MPI processor grid
create_atoms    1 box
Created 1020 atoms

mass            * 1.0

pair_style      lj/cut ${rc}
pair_style      lj/cut 2.5
pair_coeff      * * 1 1

region		lower block INF INF INF 0.0 INF INF
region		upper block INF INF $y INF INF INF
region		upper block INF INF 20 INF INF INF
group		lower region lower
120 atoms in group lower
group		upper region upper
120 atoms in group upper
set		group lower type 2
  120 settings made for type
set		group upper type 3
  120 settings made for type
group		wall union lower upper
240 atoms in group wall
group		flow subtract all wall
780 atoms in group flow

velocity        flow create $t 97287
velocity        flow create 1 97287
velocity	upper set ${srate} 0.0 0.0 units box
velocity	upper set 2.7 0.0 0.0 units box

compute		thermal flow temp/partial 0 1 0
compute		flow flow temp

fix             1 all nve
fix	        2 flow langevin $t $t 0.1 498094
fix	        2 flow langevin 1 $t 0.1 498094
fix	        2 flow langevin 1 1 0.1 498094
fix_modify      2 temp thermal

fix		3 wall setforce 0.0 0.0 0.0

compute         layers all chunk/atom bin/1d y center 0.05 units reduced
fix		4 all ave/chunk 20 500 10000 layers vx file profile.wall.2d

fix	        5 all enforce2d

# equilibration run

variable        ybox equal $y*ylat
variable        ybox equal 20*ylat
compute		tilt flow temp/ramp vx 0 ${srate} y 0 ${ybox} units box
compute		tilt flow temp/ramp vx 0 2.7 y 0 ${ybox} units box
compute		tilt flow temp/ramp vx 0 2.7 y 0 36.5148371670111 units box

thermo          1000
thermo_style	custom step temp c_tilt epair etotal press pxy

run	        20000
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4 -> bins = 27 34 1
Memory usage per processor = 2.7306 Mbytes
Step Temp c_tilt E_pair TotEng Press Pxy 
       0    1.1937193    2.1893943   -1.4419854  -0.24943634  -0.78936698  0.014349737 
    1000    1.3454512    1.9300306   -1.5968842  -0.25275207   0.66766599  -0.14162185 
    2000    1.4039195    1.7346977   -1.5342235  -0.13168039    1.0083734  0.018811845 
    3000    1.3945539    1.6038724   -1.5472166  -0.15402987   0.89714673  -0.21459294 
    4000    1.4507445    1.5640577   -1.5682837  -0.11896142   0.80780492  -0.11602642 
    5000    1.5081166    1.5260484   -1.4466585  0.059979546    1.5213379   0.15651364 
    6000     1.471403    1.3275791   -1.5730732  -0.10311276   0.76780953 -0.028043991 
    7000    1.5811576    1.3851463   -1.5518076  0.027799848    1.0149281  0.004725238 
    8000    1.5298095    1.3333038    -1.536974 -0.0086643578    1.2325979  -0.11754624 
    9000    1.5269137     1.253444   -1.5995915 -0.074174772   0.72678912  0.068344793 
   10000    1.6201621    1.2415469   -1.4659459   0.15262788    1.4780324   0.12762214 
   11000    1.6422795    1.2595346   -1.5659612  0.074708257    1.0471534 -0.039697954 
   12000    1.7111306    1.1978075   -1.5685671   0.14088596   0.97371007  0.099889098 
   13000    1.6871075    1.1495076   -1.4967158   0.18873768    1.3445558 -0.058891196 
   14000    1.7237433    1.1976445   -1.5857394   0.13631394   0.96603231  0.082195882 
   15000    1.7080799    1.1550766   -1.4962561   0.21014912    1.3733324  0.062008565 
   16000    1.7030363    1.1186642   -1.5735945   0.12777215    1.0071474  -0.12038271 
   17000    1.7442786    1.1134856   -1.5544631   0.18810536   0.98640596  -0.10793154 
   18000    1.7433517    1.0565945   -1.4702226   0.27141996    1.5983127   -0.1847178 
   19000    1.7909641     1.071494   -1.5628363   0.22637195    1.0487763  -0.16215298 
   20000    1.8291721    1.1152277   -1.4955372   0.33184161    1.4404718   0.13157652 
Loop time of 4.60977 on 1 procs for 20000 steps with 1020 atoms

Performance: 1874278.390 tau/day, 4338.607 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.2771     | 2.2771     | 2.2771     |   0.0 | 49.40
Neigh   | 0.77127    | 0.77127    | 0.77127    |   0.0 | 16.73
Comm    | 0.08461    | 0.08461    | 0.08461    |   0.0 |  1.84
Output  | 0.00045896 | 0.00045896 | 0.00045896 |   0.0 |  0.01
Modify  | 1.3487     | 1.3487     | 1.3487     |   0.0 | 29.26
Other   |            | 0.1277     |            |       |  2.77

Nlocal:    1020 ave 1020 max 1020 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    319 ave 319 max 319 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    6977 ave 6977 max 6977 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 6977
Ave neighs/atom = 6.8402
Neighbor list builds = 3091
Dangerous builds = 0

# data gathering run

variable	visc equal -pxy/(v_srate/ly)
fix		vave all ave/time 1000 1 1000 v_visc ave running

thermo_style	custom step temp pxy v_visc f_vave
thermo_modify	temp tilt
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)

# only need to run for 5000 steps to make a good 100-frame movie

#dump	        1 all custom 50 dump.wall.2d id type x y z vx

#dump		2 all image 50 image.*.jpg vx type zoom 1.6 adiam 1.2
#dump_modify	2 pad 5 amap 0.0 ${srate} ca 0.0 2 min blue max red

run		50000
Memory usage per processor = 2.73133 Mbytes
Step Temp Pxy v_visc f_vave 
   20000    1.1152277   0.14873839   -2.5647136   -2.5647136 
   21000    1.0675243 -0.064336523    1.1093622  -0.72767568 
   22000    1.1044647 -0.092189802    1.5896396  0.044762746 
   23000    1.0278193  -0.16030404    2.7641414   0.72460741 
   24000     1.032998 -0.025162118   0.43387337    0.6664606 
   25000     1.012257   0.15289388   -2.6363671   0.11598931 
   26000    1.0678095  -0.15317374    2.6411929   0.47673268 
   27000   0.99951185 -0.013635884   0.23512515   0.44653174 
   28000    1.0663423 -0.061009474    1.0519935   0.51380527 
   29000    1.0753719 -0.037018843   0.63832026   0.52625677 
   30000    1.0749259 -0.0092916614   0.16021721   0.49298044 
   31000    1.0171594  -0.14103555    2.4318926   0.65455646 
   32000    1.0811717  -0.22037237    3.7999068   0.89650648 
   33000    1.0123567 -0.076368085    1.3168239   0.92652915 
   34000    1.0923478 -0.017551868   0.30264892   0.88493714 
   35000    1.0252013 0.0042522796 -0.073322558   0.82504591 
   36000    1.0205412  -0.17942577    3.0938596   0.95850554 
   37000     1.016861  -0.15185242    2.6184092    1.0507224 
   38000    1.0156825 -0.058057333    1.0010894    1.0481101 
   39000    1.0299458 -0.028138186   0.48519005    1.0199641 
   40000    1.0109947  0.069370747   -1.1961679   0.91443404 
   41000   0.99255941  -0.20057649    3.4585639    1.0300763 
   42000   0.93280953  -0.20797609    3.5861562    1.1412102 
   43000   0.98040039  0.070643632   -1.2181165    1.0429049 
   44000     1.001795  -0.06620924    1.1416537    1.0468549 
   45000   0.96231963  0.028026245  -0.48325983   0.98800432 
   46000    1.0193639  -0.15553891    2.6819757     1.050744 
   47000    1.0241202 0.0053565438 -0.092363514    1.0099187 
   48000    0.9736932   0.12643935   -2.1802085   0.89991435 
   49000   0.96326617  -0.14719163    2.5380426   0.95451862 
   50000   0.99008772   0.03563038  -0.61437884   0.90390903 
   51000    1.0689018  -0.11122259    1.9178243   0.93559388 
   52000    1.0123467  0.021882959  -0.37733044   0.89580829 
   53000    1.0075671   0.20840798   -3.5936033   0.76376678 
   54000   0.97454265 -0.027528034   0.47466913   0.75550684 
   55000    1.0072632  -0.02991098   0.51575854   0.74884717 
   56000   0.94706748  -0.29624115     5.108121   0.86666538 
   57000    1.0411989 -0.043160809   0.74422691   0.86344332 
   58000    1.0040809   0.10858868   -1.8724074    0.7932933 
   59000    1.0101096  -0.17512944    3.0197775    0.8489554 
   60000   0.97394086  0.025630293  -0.44194616      0.81747 
   61000   0.97631407  -0.21776922    3.7550203   0.88741167 
   62000    0.9650689 -0.036733674   0.63340305   0.88150449 
   63000    1.0401136   0.11852825   -2.0437965   0.81502038 
   64000   0.99261276  -0.20362786    3.5111792   0.87493502 
   65000    1.0397086 -0.056685607   0.97743658   0.87716332 
   66000    1.0115793  -0.20411863    3.5196415   0.93338626 
   67000    1.1243059 -0.086897372    1.4983816   0.94515699 
   68000    1.0005962  0.081847197   -1.4113008   0.89706602 
   69000    1.0412065  -0.21375629    3.6858249   0.95284119 
   70000   0.97952466 -0.060208765    1.0381868   0.95451464 
Loop time of 11.6259 on 1 procs for 50000 steps with 1020 atoms

Performance: 1857923.682 tau/day, 4300.749 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 5.6901     | 5.6901     | 5.6901     |   0.0 | 48.94
Neigh   | 2.0175     | 2.0175     | 2.0175     |   0.0 | 17.35
Comm    | 0.21634    | 0.21634    | 0.21634    |   0.0 |  1.86
Output  | 0.00069594 | 0.00069594 | 0.00069594 |   0.0 |  0.01
Modify  | 3.3775     | 3.3775     | 3.3775     |   0.0 | 29.05
Other   |            | 0.3236     |            |       |  2.78

Nlocal:    1020 ave 1020 max 1020 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    332 ave 332 max 332 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    6969 ave 6969 max 6969 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 6969
Ave neighs/atom = 6.83235
Neighbor list builds = 8088
Dangerous builds = 0
Total wall time: 0:00:16
